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The functional role of isoprenoids and especially enzymatic prenylation in nature and human application is briefly covered, with the focus on bioinformatical, mechanistical and structural aspects of prenyltransferases and terpene synthases. These enzymes are as yet underrepresented but perspectively useful biocatalysts for C–C couplings of aromatic and isoprenoid substrates. Some examples of the successful use in chemoenzymatic synthesis are given including an application for the otherwise difficult synthesis of Kuhistanol A. Computational structure-based site-directed mutagenesis can be used for rational enzyme redesign to obtain altered substrate and product specificities, which is demonstrated for terpene cyclases.